There's no optical difference that would would make what you are suggesting be insurmountable.
The variation in actual registration distance between two Canon EOS bodies will likely be less than the slight variations we experience with film from one frame to the next as it is rolled through a film body after having been stored curled up in a canister for several weeks/months/years.
Only when we started using perfectly flat, non-moving, high resolution digital sensors and "pixel peeping" the results did the miniscule differences between one camera and the next, as well as between one lens and the next, start to matter very much.
The distance covered by one "step" of the lens' STM focusing mechanism is also likely to be a distance comparable to the manufacturing tolerance of the EF mount's registration distance.
There is a non-optical issue, though, that at first glance looks like it could prevent what you suggest from working.
Your STM lens is focus-by-wire. That means that there is no direct mechanical connection between the lens' focusing ring and the lens' AF motor. Instead, the manual focusing ring is an electrical switch that sends its position changes to the camera and the camera sends a signal back to the lens to move a certain amount.
Believe it or not, even a film camera as old as the EOS 3000N is perfectly compatible with Canon's new focus-by-wire STM lenses. So are all other EOS film cameras. When the STM lens is attached to the EOS 3000N with metering active, moving the lens' focus ring will cause the camera to send signals to the lens' AF motor to reposition the lens.
But here's where the issue comes in: Most STM lenses have the following (slightly paraphrased) statement included in the lens' handling instructions:
When the camera is turned on or when the camera is 'awakened' by pressing the shutter button halfway down when the camera is off due to the use of the auto power off function, the lens performs an initial reset of the focus lens.
This could be a fly in the ointment for obvious reasons.
It turns out, though, that the above advisement only seems to apply to STM zoom lenses and a few EF-S STM prime lenses, such as the EF-S 35mm f/2.8 Macro.
The Instructions for the EF 50mm f/1.8 STM include no such warning. Nor do the instructions for any of the other STM lenses I looked at that are prime, rather than zoom, lenses.
You should be fine.
As always, though, there's nothing to keep you from testing this method ahead of time just to be sure. Even if the night sky where you are is not as dark as where you will be going, you can still use the brightest stars in the sky to focus your lens using your Rebel T6/1300D and then place the focused lens on your 3000N and take a few test shots. I'd do it two or three times, with 2-3 test shots each time. Just write down your frame numbers for each test cycle so that you know what you're looking at when your film is developed and printed.